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3. In Silico Evaluation of Binding of 2-Deoxy-D-Glucose with Mpro of nCoV to Combat COVID-19

Author

Anirudh Pratap Singh Raman, Kamlesh Kumari, Pallavi Jain, Vijay Kumar Vishvakarma, Ajay Kumar, Neha Kaushik, Eun Ha Choi, Nagendra Kumar Kaushik, and Prashant Singh

Subjects
2-deoxy-D-glucose, main protease of SARS-CoV-2, molecular docking, molecular dynamics simulations, density functional theory calculations, Pharmacy and materia medica, RS1-441
Abstract

COVID-19 has threatened the existence of humanity andthis infection occurs due to SARS-CoV-2 or novel coronavirus, was first reported in Wuhan, China. Therefore, there is a need to find a promising drug to cure the people suffering from the infection. The second wave of this viral infection was shaking the world in the first half of 2021. Drugs Controllers of India has allowed the emergency use of 2-deoxy-D-glucose (2DG) in 2021 for patients suffering from this viral infection. The potentiality of 2-deoxy-D-glucose to intervene in D-glucose metabolism exists and energy deprivation is an effective parameter to inhibit cancer cell development. Once 2DG arrives in the cells, it becomes phosphorylated to 2-deoxy-D-glucose-6-phosphate (2-DG6P), a charged molecule expressively captured inside the cells. On the other hand, 2DG lacks the ability to convert into fructose-6-phosphate, resulting in a hampering of the activity of both glucose-6-phosphate isomerase and hexokinase, and finally causing cell death. Hence, the potential and effectiveness of 2DG with the main protease (Mpro) of novel coronavirus (nCoV) should be investigated using the molecular docking and molecular dynamics (MD) simulations. The ability of 2DG to inhibit the Mpro of nCoV is compared with 2-deoxyglucose (2DAG), an acyclic molecule, and 2-deoxy-D-ribose (2DR). The binding energy of the molecules with the Mpro of nCoV is calculated using molecular docking and superimposed analysis data is obtained. The binding energy of 2DG, 2DR and 2DAG was −2.40, −2.22 and −2.88 kcal/mol respectively. Although the molecular docking does not provide reliable information, therefore, the binding affinity can be confirmed by molecular dynamics simulations. Various trajectories such as Rg, RMSD, RMSF, and hydrogen bonds are obtained from the molecular dynamics (MD) simulations. 2DG was found to be a better inhibitor than the 2DAG and 2DR based on the results obtained from the MD simulations at 300 K. Furthermore, temperature-dependent MD simulations of the Mpro of nCoV with promising 2DG was performed at 295, 310 and 315 K, and the effective binding with the Mpro of nCoV occurred at 295 K. With the use of DFT calculations, optimized geometry and localization of electron density of the frontier molecular orbitals were calculated.

Published
2022
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6. List of contributors

Author

Mona M. AbouSamra, Rajasekhar Reddy Alavala, K.K. Anagha, Sandeep Arya, A. Kishore Babu, Mona Basha, Biswajit Basu, Sankha Bhattacharya, Arunima Biswas, Roja Rani Budha, Pavan Kumar Chintamaneni, Prashant K. Deshmukh, Jidnesh B. Dharmameher, Prabhanjan S. Giram, S.K. Manirul Islam, Anu Jacob, Pallavi Jain, Goutam Kumar Jena, Rabab Kamel, Kriti Kamwar, Gurpreet Kaur, Jaspreet Kaur, Palki Sahib Kaur, Snimmer Kaur, Prakash N. Kendre, Eknath B. Kole, Ashif KTK, Aditya Kumar, Moumita Kundu, Shilpa R. Mandpe, Bibhash Chandra Mohanta, Mahesh P. More, Swarupananda Mukherjee, Jitendra B. Naik, Anagha R. Nair, Sopan S. Nangare, Roshani Pagar, Tiyas Pal, Chandrakantsing V. Pardeshi, Sagar R. Pardeshi, Rabinarayan Parhi, Dhaivat C. Parikh, Pravin O. Patil, Pritam B. Patil, Tulshidas S. Patil, Bhupendra G. Prajapati, Vipul D. Prajapati, L. Rajeshkumar, Anirudh Pratap Singh Raman, M. Ramesh, GSN Koteswara Rao, Amrita Saha, Suvendu Kumar Sahoo, P. Shailaja, Roopali Sharma, K. Shinomol George, Anoop Singh, Prashant Singh, Sudarshan Singh, Praveen Sivadasu, Sonica Sondhi, N. Vigneshwari, and Khushwant S. Yadav

Published
2023

9. List of contributors

Author

Meram S. Abdelrahman, Mohamed Addi, Muhammad Ajmal, Semra Akgönüllü, Stavros Aloizos, Ghazala Ashraf, Muhammad Asif, Ayesha Aziz, R. Geetha Balakrishna, Marcos C. Barcellos, Nilay Bereli, Suraj Bharati, Mannan Boopathi, Parya Broomandi, Lavanya C, Merve Çalışır, Samir F. de A. Cavalcante, Ahmet Cetinkaya, Savita Chaudhary, Pooja Chauhan, Wei Chen, Gulsah Congur, M. Emin Corman, Victor Barros Correia, André Valle de Bairros, Adil Denizli, Prakashkumar Dobariya, Marcelo Carneiro dos Santos, Amine Elbouzidi, Muhammed Erkek, Cem Erkmen, Liu Fangfang, Tanos Celmar Costa França, K. Ganesan, Goutam Ghosh, RamaRao Golime, Zahid Hussain, Tayyaba Iftikhar, A.R. Satvik Iyengar, Pallavi Jain, Abongile Jijana, Tunca Karasu, Jasvir Kaur, S. Irem Kaya, Tawfik A. Khattab, Jong Ryeol Kim, Vinod Kumar, Kamlesh Kumari, Kamil Kuča, Kah Hon Leong, Bo Liu, Nikiwe Mhlanga, Ntsoaki Mphuthi, Munkombwe Muchindu, Bonex Mwakikunga, Gebhu Ndlovu, Sanele Nyembe, Merve Asena Özbek, Sibel A. Ozkan, Abhay H. Pande, Lokesh K. Pandey, Rohan Prasantha Perera, Shwetharani R, Anirudh Pratap Singh Raman, Chandan Hunsur Ravikumar, Mutasem Rawas-Qalaji, Doodipala Samba Reddy, Andrés Rodríguez-Seijo, Akash S, Klaus P. Saalbach, Pichiah Saravanan, Pushpendra K. Sharma, Patrick Musyoki Shem, Siew Hoong Shuit, Lucky Sikhwivhilu, Hulya Silah, Lan Ching Sim, Alessandro B.C. Simas, Madhur Babu Singh, Naveen Singh, Prabhat K. Singh, Prashant Singh, Virendra Vikram Singh, Panagiotis Stefanopoulos, Werasak Surareungcahi, Cheng-an Tao, Vikas B. Thakare, Hnin Ei Thu, Maria Tsironi, Gustavo Andrade Ugalde, Didem Nur Unal, Bengi Uslu, Lokman Uzun, Akash Verma, Maja D. Vitorovi-Todorovi, Tamara Vujatovi-Velimirov, Shenqi Wang, and Yuan-Di Zhao

Published
2023

11. An investigation for the interaction of gamma oryzanol with the Mpro of SARS-CoV-2 to combat COVID-19: DFT, molecular docking, ADME and molecular dynamics simulations

Author

Anirudh Pratap Singh Raman, Madhur Babu Singh, Vijay Kumar Vishvakarma, Pallavi Jain, Ajay Kumar, Shallu Sachdeva, Kamlesh Kumari, and Prashant Singh

Subjects
Structural Biology, General Medicine, Molecular Biology
Abstract

COVID-19 has affected more or less every nation across the world and affected the economy very badly. Infection of this virus in human took the life of millions. We have already faced the first and the second waves of COVID-19 and recently, the nations or humanity is afraid of new strain, that is, OMICRON. Considered to highly infectious than the previous strains. Therefore, the researchers are working to find a promising molecule with no or permissible toxicity. In the present work, authors have chosen 10 molecules including the molecules used in curing the infection from nCoV. All the molecules were docked against Mpro of nCoV using iGemdock, a reliable computational tool. Based on the binding energy obtained, it can be seen that only latermovir; remdesivir; zanamivir showed better binding affinity than the gamma oryzanol, the molecule of interest in this work. These three molecules are already in use to cure the patients siffering from the infection of nCoV. But, we need a cost effective and easily available molecule to fight against this viral infection. The binding energy obtained for the formation of complex of gamma oryzanol with Mpro of nCoV through molecular docking is −118.787 kcal/mol. It forms conventional hydrogen bonds with the CYS145 (3.63 Å), LEU141 (6.46 Å) and SER144 (3.18 and 2.87 Å); forms C-H bonds with PHE140 (5.08 Å), pi-alkyl interactions with CYS145 (6.72 Å); forms alkyl interaction with PRO168 (4.08 and 6.88 Å), ALA191 (5.04 Å), LEU141 (5.96 and 6.14 Å). One interesting information is obtained that the value of log Kp of gamma oryzanol is least means more permeable to skin in comparison of other molecules used in the work. Gamma oryzanol in known for to its biological potency like it can modulate the oxidative stress as well as inflammation. DFT calculations of gamma oryzanol (GO) was made at different temperature and no change in the delocalization of electron density as well no change in free energy is observed. Molecular dynamics (MD) simulations of gamma oryzanol with the Mpro of nCoV at different temperatures was performed. The formation of the complex between GO and Mpro of CoV at 290 K, 300 K, 310 K and 320 K for 100 ns was investigated. It has been observed that the effective binding is observed at 290 K, therefore, it can be said that the inhibition of the Mpro of nCoV with GO is maximum at 290 K. Communicated by Ramaswamy H. Sarma

Published
2022
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13. An update on synthesis, properties, applications and toxicity of the ILs

Author

null Himani, Anirudh Pratap Singh Raman, Madhur Babu Singh, Pallavi Jain, Preeti Chaudhary, Indra Bahadur, Kashmiri Lal, Vinod Kumar, and Prashant Singh

Subjects
Materials Chemistry, Physical and Theoretical Chemistry, Condensed Matter Physics, Spectroscopy, Atomic and Molecular Physics, and Optics, Electronic, Optical and Magnetic Materials
Published
2022

14. DFT calculations, molecular docking and SAR investigation for the formation of eutectic mixture using thiourea and salicylic acid

Author

Anirudh Pratap Singh Raman, Madhur Babu Singh, Mansi Chaudhary, Indra Bahdur, Pallavi Jain, Neha Kaushik, Eun Ha Choi, Nagendra Kumar Kaushik, Aditya Aryan Lal, and Prashant Singh

Subjects
Materials Chemistry, Physical and Theoretical Chemistry, Condensed Matter Physics, Spectroscopy, Atomic and Molecular Physics, and Optics, Electronic, Optical and Magnetic Materials
Published
2022

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